Merge clang compilation issues fix

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@689 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 4593d69f67f52d296c33ca81a4cf801ba39dd2d7

21 files changed, 310 insertions, 1308 deletions

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 02e0c614..d2c07e48 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -55,9 +55,9 @@ else()
   LINK_DIRECTORIES(${Boost_LIBRARY_DIRS})                      
 
   message(STATUS "boost include dirs:" ${Boost_INCLUDE_DIRS})
+  message(STATUS "boost library dirs:" ${Boost_LIBRARY_DIRS})
 
   include_directories(src/common/include/)
-  include_directories(src/Alpha_shapes/include/)
   include_directories(src/Bottleneck/include/)
   include_directories(src/Contraction/include/)
   include_directories(src/Hasse_complex/include/)
@@ -73,8 +73,6 @@ else()
   add_subdirectory(src/Skeleton_blocker/example) 
   add_subdirectory(src/Contraction/example)
   add_subdirectory(src/Hasse_complex/example)
-  add_subdirectory(src/Alpha_shapes/example)
-  add_subdirectory(src/Alpha_shapes/test)
   add_subdirectory(src/Bottleneck/example)
   add_subdirectory(src/Bottleneck/test)
 
diff --git a/src/Alpha_shapes/example/CMakeLists.txt b/src/Alpha_shapes/example/CMakeLists.txt
deleted file mode 100644
index 753238a5..00000000
--- a/src/Alpha_shapes/example/CMakeLists.txt
+++ /dev/null
@@ -1,32 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesExample)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
- 
-    find_package(Eigen3 3.1.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
-
-      add_executable ( dtoffrw Delaunay_triangulation_off_rw.cpp )
-      target_link_libraries(dtoffrw  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-      add_test(dtoffrw_tore3D ${CMAKE_CURRENT_BINARY_DIR}/dtoffrw ${CMAKE_SOURCE_DIR}/data/points/tore3D_1307.off 3)
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( stfromdt Simplex_tree_from_delaunay_triangulation.cpp )
-      target_link_libraries(stfromdt  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY})
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-  endif ()
-endif()
diff --git a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp b/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
deleted file mode 100644
index 03f6440d..00000000
--- a/src/Alpha_shapes/example/Delaunay_triangulation_off_rw.cpp
+++ /dev/null
@@ -1,105 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  T dt(dimension);
-  std::string offFileName(argv[1]);
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(offFileName, dt, true, true);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << offFileName << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  // Points list
-  /*for (T::Vertex_iterator vit = dt.vertices_begin(); vit != dt.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          std::cout << *Coord << " ";
-        }
-        std::cout << std::endl;
-  }
-  std::cout << std::endl;*/
- 
-  int i = 0, j = 0;
-  typedef T::Full_cell_iterator Full_cell_iterator;
-  typedef T::Facet Facet;
-
-  for (Full_cell_iterator cit = dt.full_cells_begin(); cit != dt.full_cells_end(); ++cit) {
-    if (!dt.is_infinite(cit)) {
-      j++;
-      continue;
-    }
-    Facet fct(cit, cit->index(dt.infinite_vertex()));
-    i++;
-  }
-  std::cout << "There are " << i << " facets on the convex hull." << std::endl;
-  std::cout << "There are " << j << " facets not on the convex hull." << std::endl;
-
-
-  std::string offOutputFile("out.off");
-  Gudhi::alphashapes::Delaunay_triangulation_off_writer<T> off_writer(offOutputFile, dt);
-
-  return 0;
-}
\ No newline at end of file
diff --git a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp b/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
deleted file mode 100644
index 3a17b519..00000000
--- a/src/Alpha_shapes/example/Simplex_tree_from_delaunay_triangulation.cpp
+++ /dev/null
@@ -1,103 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2014  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-void usage(char * const progName) {
-  std::cerr << "Usage: " << progName << " filename.off dimension" << std::endl;
-  exit(-1); // ----- >>
-}
-
-int main(int argc, char **argv) {
-  if (argc != 3) {
-    std::cerr << "Error: Number of arguments (" << argc << ") is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  int dimension = 0;
-  int returnedScanValue = sscanf(argv[2], "%d", &dimension);
-  if ((returnedScanValue == EOF) || (dimension <= 0)) {
-    std::cerr << "Error: " << argv[2] << " is not correct" << std::endl;
-    usage(argv[0]);
-  }
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delaunay triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(dimension);
-  std::string off_file_name(argv[1]);
-
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, false, false);
-  if (!off_reader.is_valid()) {
-    std::cerr << "Unable to read file " << off_file_name << std::endl;
-    exit(-1); // ----- >>
-  }
-
-  std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-  std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-  std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-  //std::cout << alpha_shapes_from_dt << std::endl;
-
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, dimension);
-  //std::cout << alpha_shapes_from_file << std::endl;
-  
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-
-  return 0;
-}
\ No newline at end of file
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
deleted file mode 100644
index b8efdb4d..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes.h
+++ /dev/null
@@ -1,200 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#ifndef SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
-
-// to construct a Delaunay_triangulation from a OFF file
-#include <gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h>
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include <gudhi/graph_simplicial_complex.h>
-#include <gudhi/Simplex_tree.h>
-
-#include <stdio.h>
-#include <stdlib.h>
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-#include <vector>
-#include <string>
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/** \defgroup alpha_shapes Alpha shapes in dimension N
- *
- <DT>Implementations:</DT>
- Alpha shapes in dimension N are a subset of Delaunay Triangulation in dimension N.
-
-
- * \author    Vincent Rouvreau
- * \version   1.0
- * \date      2015
- * \copyright GNU General Public License v3.
- * @{
- */
-
-/**
- * \brief Alpha shapes data structure.
- *
- * \details Every simplex \f$[v_0, \cdots ,v_d]\f$ admits a canonical orientation
- * induced by the order relation on vertices \f$ v_0 < \cdots < v_d \f$.
- *
- * Details may be found in \cite boissonnatmariasimplextreealgorithmica.
- *
- * \implements FilteredComplex
- *
- */
-class Alpha_shapes {
- private:
-  // From Simplex_tree
-  /** \brief Type required to insert into a simplex_tree (with or without subfaces).*/
-  typedef std::vector<Vertex_handle> typeVectorVertex;
-
-  // From CGAL
-  /** \brief Kernel for the Delaunay_triangulation.
-   * Dimension can be set dynamically.
-   */
-  typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > Kernel;
-  /** \brief Delaunay_triangulation type required to create an alpha-shape.
-   */
-  typedef CGAL::Delaunay_triangulation<Kernel> Delaunay_triangulation;
-
- private:
-  /** \brief Upper bound on the simplex tree of the simplicial complex.*/
-  Gudhi::Simplex_tree<> _st;
-
- public:
-
-  Alpha_shapes(std::string off_file_name, int dimension) {
-    Delaunay_triangulation dt(dimension);
-    Gudhi::alphashapes::Delaunay_triangulation_off_reader<Delaunay_triangulation>
-        off_reader(off_file_name, dt, true, true);
-    if (!off_reader.is_valid()) {
-      std::cerr << "Unable to read file " << off_file_name << std::endl;
-      exit(-1); // ----- >>
-    }
-#ifdef DEBUG_TRACES
-    std::cout << "number of vertices=" << dt.number_of_vertices() << std::endl;
-    std::cout << "number of full cells=" << dt.number_of_full_cells() << std::endl;
-    std::cout << "number of finite full cells=" << dt.number_of_finite_full_cells() << std::endl;
-#endif  // DEBUG_TRACES
-    init<Delaunay_triangulation>(dt);
-  }
-
-  template<typename T>
-  Alpha_shapes(T triangulation) {
-    init<T>(triangulation);
-  }
-
-  ~Alpha_shapes() { }
-
- private:
-
-  template<typename T>
-  void init(T triangulation) {
-    _st.set_dimension(triangulation.maximal_dimension());
-    _st.set_filtration(0.0);
-    // triangulation points list
-    for (auto vit = triangulation.finite_vertices_begin();
-         vit != triangulation.finite_vertices_end(); ++vit) {
-      typeVectorVertex vertexVector;
-      Vertex_handle vertexHdl = std::distance(triangulation.finite_vertices_begin(), vit);
-      vertexVector.push_back(vertexHdl);
-
-      // Insert each point in the simplex tree
-      _st.insert_simplex(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "P" << vertexHdl << ":";
-      for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-        std::cout << *Coord << " ";
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-    // triangulation finite full cells list
-    for (auto cit = triangulation.finite_full_cells_begin();
-         cit != triangulation.finite_full_cells_end(); ++cit) {
-      typeVectorVertex vertexVector;
-      for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-        // Vertex handle is distance - 1
-        Vertex_handle vertexHdl = std::distance(triangulation.vertices_begin(), *vit) - 1;
-        vertexVector.push_back(vertexHdl);
-      }
-      // Insert each point in the simplex tree
-      _st.insert_simplex_and_subfaces(vertexVector, 0.0);
-
-#ifdef DEBUG_TRACES
-      std::cout << "C" << std::distance(triangulation.finite_full_cells_begin(), cit) << ":";
-      for (auto value : vertexVector) {
-        std::cout << value << ' ';
-      }
-      std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    }
-  }
-
- public:
-
-  /** \brief Returns the number of vertices in the complex. */
-  size_t num_vertices() {
-    return _st.num_vertices();
-  }
-
-  /** \brief Returns the number of simplices in the complex.
-   *
-   * Does not count the empty simplex. */
-  const unsigned int& num_simplices() const {
-    return _st.num_simplices();
-  }
-
-  /** \brief Returns an upper bound on the dimension of the simplicial complex. */
-  int dimension() {
-    return _st.dimension();
-  }
-
-  /** \brief Returns an upper bound of the filtration values of the simplices. */
-  Filtration_value filtration() {
-    return _st.filtration();
-  }
-
-  friend std::ostream& operator<<(std::ostream& os, const Alpha_shapes& alpha_shape) {
-    // TODO: Program terminated with signal SIGABRT, Aborted - Maybe because of copy constructor
-    Gudhi::Simplex_tree<> st = alpha_shape._st;
-    os << st << std::endl;
-    return os;
-  }
-};
-
-} // namespace alphashapes
-
-} // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_H_
diff --git a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h b/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
deleted file mode 100644
index 693b393e..00000000
--- a/src/Alpha_shapes/include/gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h
+++ /dev/null
@@ -1,213 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-#ifndef SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-#define SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
-
-#include <string>
-#include <vector>
-#include <fstream>
-
-#include "gudhi/Off_reader.h"
-
-namespace Gudhi {
-
-namespace alphashapes {
-
-/**
- *@brief Off reader visitor with flag that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_flag_visitor_reader {
-  Complex& complex_;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-
- public:
-  explicit Delaunay_triangulation_off_flag_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    complex_.insert(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Off reader visitor that can be passed to Off_reader to read a Delaunay_triangulation_complex.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_visitor_reader {
-  Complex& complex_;
-  // typedef typename Complex::Vertex_handle Vertex_handle;
-  // typedef typename Complex::Simplex_handle Simplex_handle;
-  typedef typename Complex::Point Point;
-
-  const bool load_only_points_;
-  std::vector<Point> points_;
-  // std::vector<Simplex_handle> maximal_faces_;
-
- public:
-  explicit Delaunay_triangulation_off_visitor_reader(Complex& complex, bool load_only_points = false) :
-      complex_(complex),
-      load_only_points_(load_only_points) { }
-
-  void init(int dim, int num_vertices, int num_faces, int num_edges) {
-#ifdef DEBUG_TRACES
-    std::cout << "init - " << num_vertices << std::endl;
-#endif  // DEBUG_TRACES
-    // maximal_faces_.reserve(num_faces);
-    points_.reserve(num_vertices);
-  }
-
-  void point(const std::vector<double>& point) {
-#ifdef DEBUG_TRACES
-    std::cout << "p ";
-    for (auto coordinate: point) {
-      std::cout << coordinate << " | ";
-    }
-    std::cout << std::endl;
-#endif  // DEBUG_TRACES
-    points_.emplace_back(Point(point.size(), point.begin(), point.end()));
-  }
-
-  void maximal_face(const std::vector<int>& face) {
-    // For alpha shapes, only points are read
-  }
-
-  void done() {
-    complex_.insert(points_.begin(), points_.end());
-#ifdef DEBUG_TRACES
-    std::cout << "done" << std::endl;
-#endif  // DEBUG_TRACES
-  }
-};
-
-/**
- *@brief Class that allows to load a Delaunay_triangulation_complex from an off file.
- */
-template<typename Complex>
-class Delaunay_triangulation_off_reader {
- public:
-  /**
-   * name_file : file to read
-   * read_complex : complex that will receive the file content
-   * read_only_points : specify true if only the points must be read
-   */
-  Delaunay_triangulation_off_reader(const std::string & name_file, Complex& read_complex, bool read_only_points = false,
-                                    bool is_flag = false) : valid_(false) {
-    std::ifstream stream(name_file);
-    if (stream.is_open()) {
-      if (is_flag) {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_flag_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      } else {
-        // For alpha shapes, only points are read
-        Delaunay_triangulation_off_visitor_reader<Complex> off_visitor(read_complex, true);
-        Off_reader off_reader(stream);
-        valid_ = off_reader.read(off_visitor);
-      }
-    }
-  }
-
-  /**
-   * return true if reading did not meet problems.
-   */
-  bool is_valid() const {
-    return valid_;
-  }
-
- private:
-  bool valid_;
-};
-
-template<typename Complex>
-class Delaunay_triangulation_off_writer {
- public:
-  /**
-   * name_file : file where the off will be written
-   * save_complex : complex that be outputted in the file
-   * for now only save triangles.
-   */
-  Delaunay_triangulation_off_writer(const std::string & name_file, const Complex& save_complex) {
-    std::ofstream stream(name_file);
-    if (stream.is_open()) {
-      // OFF header
-      stream << "OFF" << std::endl;
-      // no endl on next line - don't know why...
-      stream << save_complex.number_of_vertices() << " " << save_complex.number_of_finite_full_cells() << " 0";
-
-      // Points list
-      for (auto vit = save_complex.vertices_begin(); vit != save_complex.vertices_end(); ++vit) {
-        for (auto Coord = vit->point().cartesian_begin(); Coord != vit->point().cartesian_end(); ++Coord) {
-          stream << *Coord << " ";
-        }
-        stream << std::endl;
-      }
-
-      // Finite cells list
-      for (auto cit = save_complex.finite_full_cells_begin(); cit != save_complex.finite_full_cells_end(); ++cit) {
-        stream << std::distance(cit->vertices_begin(), cit->vertices_end()) << " ";  // Dimension
-        for (auto vit = cit->vertices_begin(); vit != cit->vertices_end(); ++vit) {
-          auto vertexHdl = *vit;
-          // auto vertexHdl = std::distance(save_complex.vertices_begin(), *vit) - 1;
-          // stream << std::distance(save_complex.vertices_begin(), *(vit)) - 1 << " ";
-        }
-        stream << std::endl;
-      }
-      stream.close();
-    } else {
-      std::cerr << "could not open file " << name_file << std::endl;
-    }
-  }
-};
-
-}  // namespace alphashapes
-
-}  // namespace Gudhi
-
-#endif  // SRC_ALPHA_SHAPES_INCLUDE_GUDHI_ALPHA_SHAPES_DELAUNAY_TRIANGULATION_OFF_IO_H_
diff --git a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp b/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
deleted file mode 100644
index b4c32321..00000000
--- a/src/Alpha_shapes/test/Alpha_shapes_unit_test.cpp
+++ /dev/null
@@ -1,126 +0,0 @@
-/*    This file is part of the Gudhi Library. The Gudhi library
- *    (Geometric Understanding in Higher Dimensions) is a generic C++
- *    library for computational topology.
- *
- *    Author(s):       Vincent Rouvreau
- *
- *    Copyright (C) 2015  INRIA Saclay (France)
- *
- *    This program is free software: you can redistribute it and/or modify
- *    it under the terms of the GNU General Public License as published by
- *    the Free Software Foundation, either version 3 of the License, or
- *    (at your option) any later version.
- *
- *    This program is distributed in the hope that it will be useful,
- *    but WITHOUT ANY WARRANTY; without even the implied warranty of
- *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- *    GNU General Public License for more details.
- *
- *    You should have received a copy of the GNU General Public License
- *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
- */
-
-#define BOOST_TEST_MODULE alpha_shapes test
-#include <boost/test/included/unit_test.hpp>
-#include <boost/system/error_code.hpp>
-#include <boost/chrono/thread_clock.hpp>
-// to construct a Delaunay_triangulation from a OFF file
-#include "gudhi/Alpha_shapes/Delaunay_triangulation_off_io.h"
-#include "gudhi/Alpha_shapes.h"
-
-// to construct a simplex_tree from Delaunay_triangulation
-#include "gudhi/graph_simplicial_complex.h"
-#include "gudhi/Simplex_tree.h"
-
-#include <CGAL/Delaunay_triangulation.h>
-#include <CGAL/Epick_d.h>
-#include <CGAL/point_generators_d.h>
-#include <CGAL/algorithm.h>
-#include <CGAL/assertions.h>
-
-#include <iostream>
-#include <iterator>
-
-#include <stdio.h>
-#include <stdlib.h>
-#include <string>
-
-// Use dynamic_dimension_tag for the user to be able to set dimension
-typedef CGAL::Epick_d< CGAL::Dynamic_dimension_tag > K;
-typedef CGAL::Delaunay_triangulation<K> T;
-// The triangulation uses the default instanciation of the 
-// TriangulationDataStructure template parameter
-
-BOOST_AUTO_TEST_CASE( OFF_file ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a OFF file
-  //
-  // ----------------------------------------------------------------------------
-  std::string off_file_name("S4_100.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_file(off_file_name, 4);
-
-  const int DIMENSION = 4;
-  std::cout << "alpha_shapes_from_file.dimension()=" << alpha_shapes_from_file.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_file.filtration()=" << alpha_shapes_from_file.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.filtration() == FILTRATION);
-  
-  const int NUMBER_OF_VERTICES = 100;
-  std::cout << "alpha_shapes_from_file.num_vertices()=" << alpha_shapes_from_file.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 6779;
-  std::cout << "alpha_shapes_from_file.num_simplices()=" << alpha_shapes_from_file.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_file.num_simplices() == NUMBER_OF_SIMPLICES);
-
-}
-
-BOOST_AUTO_TEST_CASE( Delaunay_triangulation ) {
-  // ----------------------------------------------------------------------------
-  //
-  // Init of an alpha-shape from a Delauny triangulation
-  //
-  // ----------------------------------------------------------------------------
-  T dt(8);
-  std::string off_file_name("S8_10.off");
-  std::cout << "========== OFF FILE NAME = " << off_file_name << " ==========" << std::endl;
-  
-  Gudhi::alphashapes::Delaunay_triangulation_off_reader<T> off_reader(off_file_name, dt, true, true);
-  std::cout << "off_reader.is_valid()=" << off_reader.is_valid() << std::endl;
-  BOOST_CHECK(off_reader.is_valid());
-
-  const int NUMBER_OF_VERTICES = 10;
-  std::cout << "dt.number_of_vertices()=" << dt.number_of_vertices() << std::endl;
-  BOOST_CHECK(dt.number_of_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_FULL_CELLS = 30;
-  std::cout << "dt.number_of_full_cells()=" << dt.number_of_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_full_cells() == NUMBER_OF_FULL_CELLS);
-  
-  const int NUMBER_OF_FINITE_FULL_CELLS = 6;
-  std::cout << "dt.number_of_finite_full_cells()=" << dt.number_of_finite_full_cells() << std::endl;
-  BOOST_CHECK(dt.number_of_finite_full_cells() == NUMBER_OF_FINITE_FULL_CELLS);
-
-  Gudhi::alphashapes::Alpha_shapes alpha_shapes_from_dt(dt);
-
-  const int DIMENSION = 8;
-  std::cout << "alpha_shapes_from_dt.dimension()=" << alpha_shapes_from_dt.dimension() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.dimension() == DIMENSION);
-  
-  const double FILTRATION = 0.0;
-  std::cout << "alpha_shapes_from_dt.filtration()=" << alpha_shapes_from_dt.filtration() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.filtration() == FILTRATION);
-  
-  std::cout << "alpha_shapes_from_dt.num_vertices()=" << alpha_shapes_from_dt.num_vertices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_vertices() == NUMBER_OF_VERTICES);
-  
-  const int NUMBER_OF_SIMPLICES = 997;
-  std::cout << "alpha_shapes_from_dt.num_simplices()=" << alpha_shapes_from_dt.num_simplices() << std::endl;
-  BOOST_CHECK(alpha_shapes_from_dt.num_simplices() == NUMBER_OF_SIMPLICES);
-}
-
diff --git a/src/Alpha_shapes/test/CMakeLists.txt b/src/Alpha_shapes/test/CMakeLists.txt
deleted file mode 100644
index e0d33827..00000000
--- a/src/Alpha_shapes/test/CMakeLists.txt
+++ /dev/null
@@ -1,48 +0,0 @@
-cmake_minimum_required(VERSION 2.6)
-project(GUDHIAlphaShapesUT)
-
-# need CGAL 4.6
-# cmake -DCGAL_DIR=~/workspace/CGAL-4.6-beta1 ../../..
-if(CGAL_FOUND)
-  if (NOT CGAL_VERSION VERSION_LESS 4.6.0)
-    message(STATUS "CGAL version: ${CGAL_VERSION}.")
-
-    include( ${CGAL_USE_FILE} )
- 
-    find_package(Eigen3 3.1.0)
-    if (EIGEN3_FOUND)
-      message(STATUS "Eigen3 version: ${EIGEN3_VERSION}.")
-      include( ${EIGEN3_USE_FILE} )
-      include_directories (BEFORE "../../include")
-
-      if (GCOVR_PATH)
-        # for gcovr to make coverage reports - Corbera Jenkins plugin
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fprofile-arcs -ftest-coverage")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -fprofile-arcs -ftest-coverage")
-      endif()
-      if (GPROF_PATH)
-        # for gprof to make coverage reports - Jenkins
-        set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pg")
-        set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -pg")
-        set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -pg")
-      endif()
-
-      # uncomment to display debug traces
-      # add_definitions(-DDEBUG_TRACES)
-      add_executable ( AlphaShapesUT Alpha_shapes_unit_test.cpp )
-      target_link_libraries(AlphaShapesUT  ${Boost_SYSTEM_LIBRARY} ${CGAL_LIBRARY} ${Boost_UNIT_TEST_FRAMEWORK_LIBRARY})
-      add_test(NAME AlphaShapesUT 
-        COMMAND ${CMAKE_CURRENT_BINARY_DIR}/AlphaShapesUT
-        # XML format for Jenkins xUnit plugin 
-        --log_format=XML --log_sink=${CMAKE_SOURCE_DIR}/AlphaShapesUT.xml --log_level=test_suite --report_level=no)
-
-
-    else()
-      message(WARNING "Eigen3 not found. Version 3.1.0 is required for Alpha shapes feature.")
-    endif()
-  else()
-    message(WARNING "CGAL version: ${CGAL_VERSION} is too old to compile Alpha shapes feature. Version 4.6.0 is required.")
-  endif ()
-endif()
-
diff --git a/src/Alpha_shapes/test/README b/src/Alpha_shapes/test/README
deleted file mode 100644
index cddd46ca..00000000
--- a/src/Alpha_shapes/test/README
+++ /dev/null
@@ -1,14 +0,0 @@
-To compile:
-***********
-
-cd /path-to-gudhi/
-cmake .
-cd /path-to-test/
-make
-
-To launch with details:
-***********************
-
-./AlphaShapesUT --report_level=detailed --log_level=all 
-
-   ==> echo $? returns 0 in case of success (non-zero otherwise)
diff --git a/src/Alpha_shapes/test/S4_100.off b/src/Alpha_shapes/test/S4_100.off
deleted file mode 100644
index 0a5dc58c..00000000
--- a/src/Alpha_shapes/test/S4_100.off
+++ /dev/null
@@ -1,102 +0,0 @@
-OFF
-100 0 0
-0.562921 -0.735261 -0.256472 0.277007
--0.803733 -0.0527915 -0.315125 0.501918
--0.24946 -0.354982 -0.410773 -0.801887
-0.916381 -0.0512295 0.371049 0.141223
-0.182222 0.940836 -0.171362 -0.228599
--0.787145 -0.129213 0.568102 -0.202402
-0.0187866 -0.22093 -0.832882 -0.507095
--0.4702 -0.533814 0.353776 0.607286
--0.159798 -0.504771 0.263586 0.806346
-0.295546 0.162541 0.452931 0.825279
-0.242043 -0.107437 -0.913612 -0.308521
-0.875759 -0.113035 -0.469189 -0.0114505
-0.547877 -0.762247 -0.256972 -0.229729
--0.172302 0.521057 0.412013 -0.727363
--0.724729 -0.0574074 -0.0290602 0.686023
-0.700434 -0.102636 0.687285 0.162779
--0.681386 0.0946893 0.610047 0.393178
--0.847553 -0.357132 0.383743 0.0827718
-0.72297 -0.161631 -0.608517 0.284424
-0.757394 0.141549 0.196065 -0.606528
-0.78094 0.00901997 0.434536 0.448586
-0.14166 -0.619339 0.614589 -0.467582
-0.473105 -0.537832 -0.0103746 0.697711
--0.208004 0.536218 0.818027 0.00605288
-0.743694 -0.628926 0.188072 0.126488
--0.462228 -0.278147 0.35514 -0.76345
--0.17361 0.249211 0.758567 -0.57648
-0.416958 -0.254924 -0.576373 -0.654946
--0.590751 -0.286089 -0.424896 0.623402
--0.639538 -0.739693 -0.203745 0.0482932
-0.0731787 0.132121 0.864022 0.480266
--0.149644 -0.164724 -0.249746 -0.94239
--0.348592 0.0120379 -0.928656 -0.126239
-0.395328 -0.54513 0.149976 -0.723917
--0.974164 0.14707 0.157191 0.068302
--0.166425 0.119943 -0.627304 -0.751269
-0.031947 -0.358518 -0.708301 -0.607251
-0.93781 -0.155368 -0.30951 0.0240237
-0.276094 -0.753155 -0.597088 -0.00387459
--0.642876 -0.200551 -0.263517 -0.690687
-0.178711 0.604987 -0.262989 0.729993
--0.520347 0.497922 -0.676144 0.155374
--0.703999 0.500219 -0.484381 0.139789
--0.131013 0.835735 0.506779 0.166004
--0.536116 -0.566557 0.229226 0.582279
--0.334105 0.158252 0.926091 0.0754059
--0.0362677 0.296076 0.897108 0.325915
--0.57486 0.798575 0.15324 -0.0912754
-0.498602 0.0186805 0.72824 0.469801
--0.960329 0.0473356 0.261005 -0.0860505
-0.899134 -0.381392 -0.214508 0.00921711
-0.570576 0.567224 0.393019 -0.445237
--0.761763 -0.614589 -0.0546476 -0.197513
-0.188584 0.289531 0.174031 0.922129
--0.458506 -0.583876 0.639297 -0.2004
-0.785343 -0.21571 0.0794082 -0.574804
-0.0819036 0.65961 -0.247426 0.704973
-0.573125 0.49706 0.373026 0.534145
--0.513286 -0.626226 0.208535 -0.548536
-0.460558 0.468686 0.507832 -0.55707
-0.716158 -0.488201 0.388209 -0.313164
-0.881074 0.152441 0.380128 -0.236589
-0.885793 0.0386389 0.161009 -0.433537
--0.365162 0.298384 0.292846 0.831784
-0.364934 0.632269 -0.197205 -0.654346
--0.31469 -0.429991 0.665304 -0.522923
--0.734198 0.462914 -0.135691 -0.477756
--0.422885 0.674444 -0.364143 -0.483419
-0.829218 -0.154622 -0.381147 0.378439
-0.887881 0.310479 -0.109528 0.321363
--0.354398 -0.693974 0.456019 -0.429941
--0.492045 -0.160008 0.044387 0.854587
-0.0595532 0.158421 0.412577 -0.895062
--0.211441 0.491794 -0.153521 0.83058
--0.33558 -0.504711 0.353831 -0.71236
--0.735211 -0.197714 0.525626 0.379593
-0.465818 -0.424245 0.769469 -0.104627
--0.641071 -0.286339 -0.704442 -0.103923
--0.00446569 0.0249849 -0.194417 -0.980591
--0.610081 -0.252448 0.176698 -0.729966
--0.0859217 -0.154471 0.715027 0.676382
-0.091315 0.0723382 -0.855023 -0.505337
-0.165362 0.200983 -0.428242 -0.865373
--0.587465 0.303019 -0.152442 0.734729
-0.454946 -0.319828 0.437063 -0.706902
--0.384368 0.277509 0.879225 -0.0470385
-0.523335 -0.330233 -0.208592 0.757335
-0.895086 0.0448492 0.268089 -0.353466
--0.0272491 -0.567336 -0.72254 -0.39411
--0.0745014 -0.121818 -0.882466 0.448179
-0.382304 -0.240135 0.851109 -0.267941
--0.418057 -0.852847 -0.3128 0.00606452
--0.554046 0.304237 0.272381 -0.725453
-0.155115 -0.0894732 -0.245017 -0.952838
-0.114459 -0.130722 0.953669 0.245614
-0.0913002 -0.462466 0.244433 0.847374
--0.198849 0.0785111 0.131441 -0.967997
--0.303154 -0.686484 0.639333 0.167604
-0.521455 0.256835 -0.0584503 -0.811606
--0.109787 0.870544 0.161523 0.451676
diff --git a/src/Alpha_shapes/test/S8_10.off b/src/Alpha_shapes/test/S8_10.off
deleted file mode 100644
index 1d67e10f..00000000
--- a/src/Alpha_shapes/test/S8_10.off
+++ /dev/null
@@ -1,12 +0,0 @@
-OFF
-10 0 0
-0.440036 -0.574754 -0.200485 0.216537 -0.501251 -0.0329236 -0.196529 0.313023
--0.129367 -0.184089 -0.213021 -0.415848 0.783529 -0.0438025 0.317256 0.120749
-0.132429 0.683748 -0.124536 -0.166133 -0.540695 -0.0887576 0.390234 -0.139031
-0.0137399 -0.161581 -0.609142 -0.370872 -0.320669 -0.364053 0.24127 0.41416
--0.115313 -0.36425 0.190208 0.581871 0.204605 0.112527 0.313562 0.571337
-0.168272 -0.0746917 -0.635156 -0.214488 0.629498 -0.0812499 -0.337255 -0.00823068
-0.369896 -0.514626 -0.173493 -0.1551 -0.127105 0.384377 0.303936 -0.536566
--0.49013 -0.0388242 -0.0196532 0.463953 0.515962 -0.0756047 0.506276 0.119908
--0.434258 0.060347 0.388793 0.250579 -0.653127 -0.275207 0.295714 0.0637842
-0.596172 -0.133284 -0.501793 0.234541 0.428452 0.0800735 0.110912 -0.343109
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 3be05c4f..9f6db2c7 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -44,7 +44,6 @@ else()
   add_subdirectory(example/Skeleton_blocker)                   
   add_subdirectory(example/Contraction)                   
   add_subdirectory(example/Hasse_complex)
-  add_subdirectory(example/Alpha_shapes)
   add_subdirectory(example/Bottleneck)
 
   # GudhUI
diff --git a/src/Contraction/example/Garland_heckbert/Error_quadric.h b/src/Contraction/example/Garland_heckbert/Error_quadric.h
index 725a3a56..72134c9d 100644
--- a/src/Contraction/example/Garland_heckbert/Error_quadric.h
+++ b/src/Contraction/example/Garland_heckbert/Error_quadric.h
@@ -122,7 +122,7 @@ public :
 	 * Return the point such that it minimizes the gradient of the quadric.

 	 * Det must be passed with the determinant value of the gradient (should be non zero).

 	 */

-	inline Point solve_linear_gradient(double det = grad_determinant()) const{

+	inline Point solve_linear_gradient(double det) const{

 		return Point({

 				(-coeff[1]*coeff[5]*coeff[8]+coeff[1]*coeff[7]*coeff[6]+coeff[2]*coeff[8]*coeff[4]-coeff[2]*coeff[5]*coeff[6]-coeff[3]*coeff[4]*coeff[7]+coeff[3]*coeff[5]*coeff[5])/ det,

 				(coeff[0]*coeff[5]*coeff[8]-coeff[0]*coeff[7]*coeff[6]-coeff[5]*coeff[2]*coeff[3]-coeff[1]*coeff[2]*coeff[8]+coeff[6]*coeff[2]*coeff[2]+coeff[1]*coeff[3]*coeff[7])/det,

diff --git a/src/GudhUI/CMakeLists.txt b/src/GudhUI/CMakeLists.txt
index ddbae969..9348868a 100644
--- a/src/GudhUI/CMakeLists.txt
+++ b/src/GudhUI/CMakeLists.txt
@@ -5,6 +5,7 @@ find_package(CGAL  COMPONENTS Qt4)
 find_package(Qt4)
 find_package(QGLViewer)
 find_package(OpenGL)
+
 message("CMAKE_CXX_FLAGS ${CMAKE_CXX_FLAGS}")
 message("CMAKE_CXX_FLAGS_DEBUG ${CMAKE_CXX_FLAGS_DEBUG}")
 message("CMAKE_CXX_FLAGS_RELEASE ${CMAKE_CXX_FLAGS_RELEASE}")
@@ -66,5 +67,5 @@ if ( CGAL_FOUND AND QT4_FOUND AND OPENGL_FOUND AND QGLVIEWER_FOUND )
   target_link_libraries( GudhUI ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} )	
 
 else()
-  message(STATUS "NOTICE: This demo requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
+  message(STATUS "NOTICE: GudhUI requires CGAL, the QGLViewer, OpenGL and Qt4, and will not be compiled.")
 endif()
diff --git a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
index b0d68f09..8bd265d8 100644
--- a/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
+++ b/src/Persistent_cohomology/include/gudhi/Persistent_cohomology.h
@@ -37,6 +37,7 @@
 #include <list>
 #include <vector>
 #include <set>
+#include <fstream>  // std::ofstream
 
 namespace Gudhi {
 
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
index aaaab8b0..6ad1fdd3 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_off_io.h
@@ -107,7 +107,7 @@ class Skeleton_blocker_off_visitor_reader {
   }
 
   void done() {
-    complex_ = make_complex_from_top_faces(maximal_faces_.begin(), maximal_faces_.end(),
+    complex_ = make_complex_from_top_faces<Complex>(maximal_faces_.begin(), maximal_faces_.end(),
                                            points_.begin(), points_.end() );
   }
 };
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
index 10d64e98..0a2fcb9a 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_simplex.h
@@ -69,7 +69,9 @@ class Skeleton_blocker_simplex {
   }
 
   Skeleton_blocker_simplex(std::initializer_list<T>& list) {
-    for_each(list.begin(), list.end(), add_vertex);
+    std::for_each(list.begin(), list.end(), [&] (T const& elt) {
+      add_vertex(elt);
+    });
   }
 
   template<typename ... Args>
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
index e906df75..40e26c68 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/Skeleton_blocker_sub_complex.h
@@ -75,25 +75,11 @@ class Skeleton_blocker_sub_complex : public ComplexType {
   typedef typename ComplexType::Root_simplex_handle Root_simplex_handle;
 
  protected:
-  ///**
-  //* @brief Returns true iff the simplex formed by all vertices contained in 'addresses_sigma_in_link'
-  //* but 'vertex_to_be_ignored' is in 'link'
-  //*/
-  /*
-   template<typename T> friend bool
-   proper_face_in_union(
-   Skeleton_blocker_sub_complex<T> & link,
-   std::vector<boost::optional<typename T::Vertex_handle> > & addresses_sigma_in_link,
-   int vertex_to_be_ignored);*/
-
+  
   /**
    * @brief Determines whether all proper faces of simplex 'sigma' belong to 'link1' \cup 'link2'
    * where 'link1' and 'link2' are subcomplexes of the same complex of type ComplexType
    */
-  // template<typename T> friend bool
-  // proper_faces_in_union(Skeleton_blocker_simplex<typename T::Root_vertex_handle> & sigma, Skeleton_blocker_sub_complex<T> & link1, Skeleton_blocker_sub_complex<T> & link2){
-  // template<typename T> friend bool
-  // proper_faces_in_union(Skeleton_blocker_simplex<typename T::Root_vertex_handle> & sigma, Skeleton_blocker_sub_complex<T> & link1, Skeleton_blocker_sub_complex<T> & link2);
   typedef std::map<Root_vertex_handle, Vertex_handle> IdAddressMap;
   typedef typename IdAddressMap::value_type AddressPair;
   typedef typename IdAddressMap::iterator IdAddressMapIterator;
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
index 666ce430..f9d4d072 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker/iterators/Skeleton_blockers_simplices_iterators.h
@@ -1,46 +1,42 @@
- /*    This file is part of the Gudhi Library. The Gudhi library
-  *    (Geometric Understanding in Higher Dimensions) is a generic C++
-  *    library for computational topology.
-  *
-  *    Author(s):       David Salinas
-  *
-  *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
-  *
-  *    This program is free software: you can redistribute it and/or modify
-  *    it under the terms of the GNU General Public License as published by
-  *    the Free Software Foundation, either version 3 of the License, or
-  *    (at your option) any later version.
-  *
-  *    This program is distributed in the hope that it will be useful,
-  *    but WITHOUT ANY WARRANTY; without even the implied warranty of
-  *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-  *    GNU General Public License for more details.
-  *
-  *    You should have received a copy of the GNU General Public License
-  *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
-  */
-#ifndef GUDHI_KELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
+/*    This file is part of the Gudhi Library. The Gudhi library
+ *    (Geometric Understanding in Higher Dimensions) is a generic C++
+ *    library for computational topology.
+ *
+ *    Author(s):       David Salinas
+ *
+ *    Copyright (C) 2014  INRIA Sophia Antipolis-Mediterranee (France)
+ *
+ *    This program is free software: you can redistribute it and/or modify
+ *    it under the terms of the GNU General Public License as published by
+ *    the Free Software Foundation, either version 3 of the License, or
+ *    (at your option) any later version.
+ *
+ *    This program is distributed in the hope that it will be useful,
+ *    but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *    GNU General Public License for more details.
+ *
+ *    You should have received a copy of the GNU General Public License
+ *    along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+#ifndef GUDHI_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
 #define GUDHI_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
 
+#include "boost/iterator/iterator_facade.hpp"
+
 #include <memory>
 #include <list>
 #include <iostream>
-#include "gudhi/Utils.h"
-#include "boost/iterator/iterator_facade.hpp"
-
 
 #include "gudhi/Skeleton_blocker_link_complex.h"
 #include "gudhi/Skeleton_blocker/Skeleton_blocker_link_superior.h"
-
 #include "gudhi/Skeleton_blocker/internal/Trie.h"
-
+#include "gudhi/Utils.h"
 
 namespace Gudhi {
 
-
 namespace skbl {
 
-
 /**
  * Link may be Skeleton_blocker_link_complex<SkeletonBlockerComplex> to iterate over all
  * simplices around a vertex OR
@@ -49,299 +45,268 @@ namespace skbl {
  * The iteration is done by computing a trie with the link and doing a breadth-first traversal
  * of the trie.
  */
-template<typename SkeletonBlockerComplex,typename Link>
+template<typename SkeletonBlockerComplex, typename Link>
 class Simplex_around_vertex_iterator :
-		public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerComplex,Link>
+public boost::iterator_facade < Simplex_around_vertex_iterator<SkeletonBlockerComplex, Link>
 , typename SkeletonBlockerComplex::Simplex_handle
 , boost::forward_traversal_tag
 , typename SkeletonBlockerComplex::Simplex_handle
->
-{
-	friend class boost::iterator_core_access;
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-	typedef typename Complex::Simplex_handle Simplex_handle;
-
-
-	typedef typename Link::Vertex_handle Link_vertex_handle;
-	// Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
-
-	typedef typename Gudhi::skbl::Trie<Simplex_handle> Trie;
-
-
-private:
-	const Complex* complex;
-	Vertex_handle v;
-	std::shared_ptr<Link> link_v;
-	std::shared_ptr<Trie> trie;
-	std::list<Trie*> nodes_to_be_seen; // todo deque
-
-public:
-	Simplex_around_vertex_iterator():complex(0){
-	}
-
-	Simplex_around_vertex_iterator(const Complex* complex_,Vertex_handle v_):
-		complex(complex_),
-		v(v_),
-		link_v(new Link(*complex_,v_)),
-		trie(new Trie(v_)){
-		compute_trie_and_nodes_to_be_seen();
-	}
-
-	// todo avoid useless copy
-	// todo currently just work if copy begin iterator
-	Simplex_around_vertex_iterator(const Simplex_around_vertex_iterator& other):
-		complex(other.complex),
-		v(other.v),
-		link_v(other.link_v),
-		trie(other.trie),
-		nodes_to_be_seen(other.nodes_to_be_seen){
-		if(!other.is_end()){
-		}
-	}
-
-	/**
-	 * returns an iterator to the end
-	 */
-	Simplex_around_vertex_iterator(const Complex* complex_,Vertex_handle v_,bool end):
-		complex(complex_),
-		v(v_){
-		set_end();
-	}
-
-private:
-
-
-	void compute_trie_and_nodes_to_be_seen(){
-		// once we go through every simplices passing through v0
-		// we remove v0. That way, it prevents from passing a lot of times
-		// though edges leaving v0.
-		// another solution would have been to provides an adjacency iterator
-		// to superior vertices that avoids lower ones.
-		while(!link_v->empty()){
-			auto v0 = *(link_v->vertex_range().begin());
-			trie->add_child(build_trie(v0,trie.get()));
-			link_v->remove_vertex(v0);
-		}
-		nodes_to_be_seen.push_back(trie.get());
-	}
-
-	Trie* build_trie(Link_vertex_handle link_vh,Trie* parent){
-		Trie* res = new Trie(parent_vertex(link_vh),parent);
-		for(Link_vertex_handle nv : link_v->vertex_range(link_vh)) {
-			if(link_vh < nv){
-				Simplex_handle simplex_node_plus_nv(res->simplex());
-				simplex_node_plus_nv.add_vertex(parent_vertex(nv));
-				if(complex->contains(simplex_node_plus_nv)){
-					res->add_child(build_trie(nv,res));
-				}
-			}
-		}
-		return res;
-	}
-
-	bool is_node_in_complex(Trie* trie){
-		return true;
-	}
-
-	Vertex_handle parent_vertex(Link_vertex_handle link_vh) const{
-		return complex->convert_handle_from_another_complex(*link_v,link_vh);
-	}
-
-
-
-public:
-
-	friend std::ostream& operator<<(std::ostream& stream, const Simplex_around_vertex_iterator& savi){
-		stream<< savi.trie<< std::endl; ;
-		stream << "("<<savi.nodes_to_be_seen.size()<<") nodes to see\n";
-		return stream;
-	}
-
-	bool equal(const Simplex_around_vertex_iterator& other) const{
-		bool same_complex = (complex == other.complex);
-		if(!same_complex)
-			return false;
-
-		if(!(v == other.v))
-			return false;
-
-		bool both_empty = nodes_to_be_seen.empty() && other.nodes_to_be_seen.empty();
-		if(both_empty)
-			return true;
-
-		bool both_non_empty = !nodes_to_be_seen.empty() && !other.nodes_to_be_seen.empty();
-
-		if(!both_non_empty) return false; //one is empty the other is not
-
-		bool same_node = (**(nodes_to_be_seen.begin()) == **(other.nodes_to_be_seen.begin()));
-		return same_node;
-	}
-
-	void increment(){
-		assert(!is_end());
-		Trie* first_node = nodes_to_be_seen.front();
-
-		nodes_to_be_seen.pop_front();
-
-		for(auto childs : first_node->childs){
-			nodes_to_be_seen.push_back(childs.get());
-		}
-
-	}
-
-	Simplex_handle dereference() const{
-		assert(!nodes_to_be_seen.empty());
-		Trie* first_node = nodes_to_be_seen.front();
-		return first_node->simplex();
-	}
-
-//private:
-	Simplex_handle get_trie_address() const{
-		assert(!nodes_to_be_seen.empty());
-		return nodes_to_be_seen.front();
-	}
-
-private:
-	void set_end(){
-		nodes_to_be_seen.clear();
-	}
-
-	bool is_end() const{
-		return nodes_to_be_seen.empty();
-	}
+> {
+  friend class boost::iterator_core_access;
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+  typedef typename Complex::Simplex_handle Simplex_handle;
+
+  // Link_vertex_handle == Complex_Vertex_handle but this renaming helps avoiding confusion
+  typedef typename Link::Vertex_handle Link_vertex_handle;
+
+  typedef typename Gudhi::skbl::Trie<Simplex_handle> Trie;
+
+ private:
+  const Complex* complex;
+  Vertex_handle v;
+  std::shared_ptr<Link> link_v;
+  std::shared_ptr<Trie> trie;
+  std::list<Trie*> nodes_to_be_seen; // todo deque
+
+ public:
+  Simplex_around_vertex_iterator() : complex(0) {}
+
+  Simplex_around_vertex_iterator(const Complex* complex_, Vertex_handle v_) :
+      complex(complex_),
+      v(v_),
+      link_v(new Link(*complex_, v_)),
+      trie(new Trie(v_)) {
+    compute_trie_and_nodes_to_be_seen();
+  }
+
+  // todo avoid useless copy
+  // todo currently just work if copy begin iterator
+  Simplex_around_vertex_iterator(const Simplex_around_vertex_iterator& other) :
+      complex(other.complex),
+      v(other.v),
+      link_v(other.link_v),
+      trie(other.trie),
+      nodes_to_be_seen(other.nodes_to_be_seen) {
+    if (!other.is_end()) {}
+  }
+
+  /**
+   * returns an iterator to the end
+   */
+  Simplex_around_vertex_iterator(const Complex* complex_, Vertex_handle v_, bool end) :
+      complex(complex_),
+      v(v_) {
+    set_end();
+  }
+
+ private:
+  void compute_trie_and_nodes_to_be_seen() {
+    // once we go through every simplices passing through v0
+    // we remove v0. That way, it prevents from passing a lot of times
+    // though edges leaving v0.
+    // another solution would have been to provides an adjacency iterator
+    // to superior vertices that avoids lower ones.
+    while (!link_v->empty()) {
+      auto v0 = *(link_v->vertex_range().begin());
+      trie->add_child(build_trie(v0, trie.get()));
+      link_v->remove_vertex(v0);
+    }
+    nodes_to_be_seen.push_back(trie.get());
+  }
+
+  Trie* build_trie(Link_vertex_handle link_vh, Trie* parent) {
+    Trie* res = new Trie(parent_vertex(link_vh), parent);
+    for (Link_vertex_handle nv : link_v->vertex_range(link_vh)) {
+      if (link_vh < nv) {
+        Simplex_handle simplex_node_plus_nv(res->simplex());
+        simplex_node_plus_nv.add_vertex(parent_vertex(nv));
+        if (complex->contains(simplex_node_plus_nv)) {
+          res->add_child(build_trie(nv, res));
+        }
+      }
+    }
+    return res;
+  }
+
+  bool is_node_in_complex(Trie* trie) {
+    return true;
+  }
+
+  Vertex_handle parent_vertex(Link_vertex_handle link_vh) const {
+    return complex->convert_handle_from_another_complex(*link_v, link_vh);
+  }
+
+ public:
+  friend std::ostream& operator<<(std::ostream& stream, const Simplex_around_vertex_iterator& savi) {
+    stream << savi.trie << std::endl;
+    stream << "(" << savi.nodes_to_be_seen.size() << ") nodes to see\n";
+    return stream;
+  }
+
+  bool equal(const Simplex_around_vertex_iterator& other) const {
+    bool same_complex = (complex == other.complex);
+    if (!same_complex)
+      return false;
+
+    if (!(v == other.v))
+      return false;
+
+    bool both_empty = nodes_to_be_seen.empty() && other.nodes_to_be_seen.empty();
+    if (both_empty)
+      return true;
+
+    bool both_non_empty = !nodes_to_be_seen.empty() && !other.nodes_to_be_seen.empty();
+
+    if (!both_non_empty) return false; //one is empty the other is not
+
+    bool same_node = (**(nodes_to_be_seen.begin()) == **(other.nodes_to_be_seen.begin()));
+    return same_node;
+  }
+
+  void increment() {
+    assert(!is_end());
+    Trie* first_node = nodes_to_be_seen.front();
+
+    nodes_to_be_seen.pop_front();
+
+    for (auto childs : first_node->childs) {
+      nodes_to_be_seen.push_back(childs.get());
+    }
+
+  }
+
+  Simplex_handle dereference() const {
+    assert(!nodes_to_be_seen.empty());
+    Trie* first_node = nodes_to_be_seen.front();
+    return first_node->simplex();
+  }
+
+  Simplex_handle get_trie_address() const {
+    assert(!nodes_to_be_seen.empty());
+    return nodes_to_be_seen.front();
+  }
+
+ private:
+  void set_end() {
+    nodes_to_be_seen.clear();
+  }
+
+  bool is_end() const {
+    return nodes_to_be_seen.empty();
+  }
 };
 
-
-
 template<typename SkeletonBlockerComplex>
 class Simplex_iterator :
-		public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
+public boost::iterator_facade < Simplex_iterator<SkeletonBlockerComplex>
 , typename SkeletonBlockerComplex::Simplex_handle
 , boost::forward_traversal_tag
 , typename SkeletonBlockerComplex::Simplex_handle
->
-{
-	typedef Skeleton_blocker_link_superior<SkeletonBlockerComplex> Link;
-
-	friend class boost::iterator_core_access;
-
-	template<class SkBlDS> friend class Skeleton_blocker_complex;
-
-
-	typedef SkeletonBlockerComplex Complex;
-	typedef typename Complex::Vertex_handle Vertex_handle;
-	typedef typename Complex::Edge_handle Edge_handle;
-	typedef typename Complex::Simplex_handle Simplex_handle;
-
-	typedef typename Complex::Complex_vertex_iterator Complex_vertex_iterator;
-
-
-	typedef typename Link::Vertex_handle Link_vertex_handle;
-
-private:
-
-	const Complex* complex_;
-	Complex_vertex_iterator current_vertex_;
-
-	typedef Simplex_around_vertex_iterator<SkeletonBlockerComplex,Link> SAVI;
-	SAVI current_simplex_around_current_vertex_;
-	SAVI simplices_around_current_vertex_end_;
-
-
-public:
-	Simplex_iterator():complex_(0){}
-
-	// should not be called if the complex is empty
-	Simplex_iterator(const Complex* complex):
-		complex_(complex),
-		current_vertex_(complex->vertex_range().begin()),
-		current_simplex_around_current_vertex_(complex,*current_vertex_),
-		simplices_around_current_vertex_end_(complex,*current_vertex_,true)
-	{
-		assert(!complex->empty());
-	}
-
-private:
-	// todo return to private
-	Simplex_iterator(const Complex* complex,bool end):
-		complex_(complex)
-	{
-		set_end();
-	}
-
-public:
-
-	Simplex_iterator(const Simplex_iterator& other)
-	:
-		complex_(other.complex_),
-		current_vertex_(other.current_vertex_),
-		current_simplex_around_current_vertex_(other.current_simplex_around_current_vertex_),
-		simplices_around_current_vertex_end_(other.simplices_around_current_vertex_end_)
-	{
-	}
-
-	friend Simplex_iterator make_begin_iterator(const Complex* complex){
-		if(complex->empty())
-			return make_end_simplex_iterator(complex);
-		else
-			return Simplex_iterator(complex);
-	}
-
-	friend Simplex_iterator make_end_simplex_iterator(const Complex* complex){
-		return Simplex_iterator(complex,true);
-	}
-
-	bool equal(const Simplex_iterator& other) const{
-		if(complex_!=other.complex_) return false;
-		if(current_vertex_!=other.current_vertex_) return false;
-		if(is_end() && other.is_end()) return true;
-		if(current_simplex_around_current_vertex_ != other.current_simplex_around_current_vertex_)
-			return false;
-		return true;
-	}
-
-	void increment(){
-		if(current_simplex_around_current_vertex_!= simplices_around_current_vertex_end_){
-			current_simplex_around_current_vertex_.increment();
-			if( current_simplex_around_current_vertex_== simplices_around_current_vertex_end_)
-				goto_next_vertex();
-		}
-		else{
-			goto_next_vertex();
-		}
-	}
-
-	void goto_next_vertex(){
-		current_vertex_.increment();
-		if(!is_end()){
-			current_simplex_around_current_vertex_= SAVI(complex_,*current_vertex_);
-			simplices_around_current_vertex_end_ = SAVI(complex_,*current_vertex_,true);
-		}
-	}
-
-	Simplex_handle dereference() const{
-		return current_simplex_around_current_vertex_.dereference();
-	}
-
-private:
-	void set_end(){
-		current_vertex_ = complex_->vertex_range().end();
-	}
-
-	bool is_end() const{
-		return (current_vertex_ == complex_->vertex_range().end());
-	}
+> {
+  typedef Skeleton_blocker_link_superior<SkeletonBlockerComplex> Link;
+
+  friend class boost::iterator_core_access;
+
+  template<class SkBlDS> friend class Skeleton_blocker_complex;
+
+  typedef SkeletonBlockerComplex Complex;
+  typedef typename Complex::Vertex_handle Vertex_handle;
+  typedef typename Complex::Edge_handle Edge_handle;
+  typedef typename Complex::Simplex_handle Simplex_handle;
+  typedef typename Complex::Complex_vertex_iterator Complex_vertex_iterator;
+  typedef typename Link::Vertex_handle Link_vertex_handle;
+
+ private:
+  const Complex* complex_;
+  Complex_vertex_iterator current_vertex_;
+
+  typedef Simplex_around_vertex_iterator<SkeletonBlockerComplex, Link> SAVI;
+  SAVI current_simplex_around_current_vertex_;
+  SAVI simplices_around_current_vertex_end_;
+
+ public:
+  Simplex_iterator() : complex_(0) { }
+
+  Simplex_iterator(const Complex* complex) :
+      complex_(complex),
+      current_vertex_(complex->vertex_range().begin()),
+      current_simplex_around_current_vertex_(complex, *current_vertex_),
+      simplices_around_current_vertex_end_(complex, *current_vertex_, true) {
+    // should not be called if the complex is empty
+    assert(!complex->empty());
+  }
+
+ private:
+  // todo return to private
+  Simplex_iterator(const Complex* complex, bool end) :
+      complex_(complex) {
+    set_end();
+  }
+
+ public:
+  Simplex_iterator(const Simplex_iterator& other)
+      :
+      complex_(other.complex_),
+      current_vertex_(other.current_vertex_),
+      current_simplex_around_current_vertex_(other.current_simplex_around_current_vertex_),
+      simplices_around_current_vertex_end_(other.simplices_around_current_vertex_end_) { }
+
+  friend Simplex_iterator make_begin_iterator(const Complex* complex) {
+    if (complex->empty())
+      return make_end_simplex_iterator(complex);
+    else
+      return Simplex_iterator(complex);
+  }
+
+  friend Simplex_iterator make_end_simplex_iterator(const Complex* complex) {
+    return Simplex_iterator(complex, true);
+  }
+
+  bool equal(const Simplex_iterator& other) const {
+    if (complex_ != other.complex_) return false;
+    if (current_vertex_ != other.current_vertex_) return false;
+    if (is_end() && other.is_end()) return true;
+    if (current_simplex_around_current_vertex_ != other.current_simplex_around_current_vertex_)
+      return false;
+    return true;
+  }
+
+  void increment() {
+    if (current_simplex_around_current_vertex_ != simplices_around_current_vertex_end_) {
+      current_simplex_around_current_vertex_.increment();
+      if (current_simplex_around_current_vertex_ == simplices_around_current_vertex_end_)
+        goto_next_vertex();
+    } else {
+      goto_next_vertex();
+    }
+  }
+
+  void goto_next_vertex() {
+    current_vertex_.increment();
+    if (!is_end()) {
+      current_simplex_around_current_vertex_ = SAVI(complex_, *current_vertex_);
+      simplices_around_current_vertex_end_ = SAVI(complex_, *current_vertex_, true);
+    }
+  }
+
+  Simplex_handle dereference() const {
+    return current_simplex_around_current_vertex_.dereference();
+  }
+
+ private:
+  void set_end() {
+    current_vertex_ = complex_->vertex_range().end();
+  }
+
+  bool is_end() const {
+    return (current_vertex_ == complex_->vertex_range().end());
+  }
 };
 
+}  // namespace skbl
 
-}
-
-} // namespace GUDHI
-
-
-
-
+}  // namespace Gudhi
 
-#endif /* SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_ */
+#endif  // GUDHI_SKELETON_BLOCKERS_SIMPLICES_ITERATORS_H_
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
index 437482cb..3eff1ba3 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_geometric_complex.h
@@ -79,23 +79,6 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
       (*this)[Vertex_handle(current++)].point() = Point(point->begin(), point->end());
   }
 
-  template<typename SimpleHandleOutputIterator, typename PointIterator>
-  friend Skeleton_blocker_geometric_complex make_complex_from_top_faces(
-                                                                        SimpleHandleOutputIterator simplex_begin,
-                                                                        SimpleHandleOutputIterator simplex_end,
-                                                                        PointIterator points_begin,
-                                                                        PointIterator points_end,
-                                                                        bool is_flag_complex = false) {
-    Skeleton_blocker_geometric_complex complex;
-    unsigned current = 0;
-    complex =
-        make_complex_from_top_faces<Skeleton_blocker_geometric_complex>(simplex_begin, simplex_end, is_flag_complex);
-    for (auto point = points_begin; point != points_end; ++point)
-      // complex.point(Vertex_handle(current++)) = Point(point->begin(),point->end());
-      complex.point(Vertex_handle(current++)) = Point(*point);
-    return complex;
-  }
-
   /**
    * @brief Constructor with a list of simplices.
    * Points of every vertex are the point constructed with default constructor.
@@ -215,6 +198,25 @@ public Skeleton_blocker_complex<SkeletonBlockerGeometricDS> {
   }
 };
 
+
+template<typename SkeletonBlockerGeometricComplex, typename SimpleHandleOutputIterator, typename PointIterator>
+SkeletonBlockerGeometricComplex make_complex_from_top_faces(
+        SimpleHandleOutputIterator simplex_begin,
+        SimpleHandleOutputIterator simplex_end,
+        PointIterator points_begin,
+        PointIterator points_end,
+        bool is_flag_complex = false) {
+  typedef SkeletonBlockerGeometricComplex SBGC;
+  SkeletonBlockerGeometricComplex complex;
+  unsigned current = 0;
+  complex =
+    make_complex_from_top_faces<SBGC>(simplex_begin, simplex_end, is_flag_complex);
+  for (auto point = points_begin; point != points_end; ++point)
+    // complex.point(Vertex_handle(current++)) = Point(point->begin(),point->end());
+    complex.point(typename SBGC::Vertex_handle(current++)) = typename SBGC::Point(*point);
+  return complex;
+}
+
 }  // namespace skbl
 
 }  // namespace Gudhi
diff --git a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
index dd8d898e..57e1daf0 100644
--- a/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
+++ b/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_simplifiable_complex.h
@@ -208,7 +208,8 @@ void Skeleton_blocker_complex<SkeletonBlockerDS>::remove_star(const Simplex_hand
 }
 
 /**
- * @brief add a maximal simplex plus all its cofaces.
+ * @brief add a maximal simplex plus all its cofaces. All vertices lower than the higher vertex of
+ * sigma must already be present.
  * @details the simplex must have dimension greater than one (otherwise use add_vertex or add_edge).
  */
 template<typename SkeletonBlockerDS>
@@ -338,9 +339,11 @@ void
 Skeleton_blocker_complex<SkeletonBlockerDS>::contract_edge(Vertex_handle a, Vertex_handle b) {
   assert(this->contains_vertex(a));
   assert(this->contains_vertex(b));
-  assert(this->contains_edge(a, b));
 
-  // if some blockers passes through 'ab', we remove them.
+  if(this->contains_edge(a, b))
+    this->add_edge(a, b);
+
+  // if some blockers passes through 'ab', we need to remove them.
   if (!link_condition(a, b))
     delete_blockers_around_edge(a, b);